Clonal evolution of somatic mosaicism during acute-to-chronic kidney disease progression

急性肾损伤通常在危重患者中观察到，并导致进行性慢性肾脏疾病或死亡的风险大大增加。急性肾损伤由复杂的病理生理过程引发，包括炎症、缺血、缺氧和/或毒素暴露。急性肾损伤导致肾小管细胞的广泛细胞死亡。存活的细胞然后克隆增殖并修复受损的肾小管。细胞应激、损伤、增殖和恢复的重复循环可能使肾细胞易于发生疾病促进性体细胞突变。肾细胞中的体细胞突变可以产生遗传上不同的细胞群（即，亚克隆），导致组织特异性的“体细胞嵌合体”。当这些突变破坏关键的表观遗传和转录程序时，它们可以产生具有不同疾病表型和机制的致病亚克隆。这一假说得到了肾脏疾病中基因组不稳定性增加的证据以及急性肾损伤或慢性肾脏疾病患者发生肾肿瘤的倾向的支持。然而，获得性体细胞嵌合体在肾组织中的作用及其潜在的病理生理学意义尚不完全清楚。在这里，我们建议联合收割机单细胞和链特异性DNA测序（即，Strand-seq）与来自肾细胞和组织的转座酶可接近染色质（ATAC）和单核RNA测序的测定一起研究单细胞水平上体细胞嵌合现象的发展和后果。我们将确定获得性体细胞结构变异的类型和频率，如缺失、插入、倒位和其他基因组重排，并将其与全基因组核小体占有率、染色质可及性和肾细胞基因表达的变化相关联。我们将比较实验条件（小鼠肾脏的体内缺血-再灌注损伤和体外模拟肾细胞缺氧）和急性或慢性肾脏疾病患者尿液中排泄的肾细胞临床样本。体细胞结构变异体对肾细胞增殖、细胞死亡和基因表达的推定影响将通过肾细胞中变异体相关分子扰动的实验建模来验证。这项研究有可能揭示肾细胞中获得性体细胞基因组改变与促进疾病的基因表达控制失调之间的新分子联系。

Acute kidney injury is commonly observed in critically ill individuals and results in a greatly increased risk of progressive chronic kidney disease or death. Acute kidney injury is initiated by complex pathophysiological processes that include inflammation, ischemia, hypoxia, and/or toxin exposure. Acute kidney injury results in widespread cell death of the cells of the renal tubule. Surviving cells then proliferate clonally and repair the injured kidney tubule. The repeated cycles of cellular stress, injury, proliferation, and recovery may predispose kidney cells to disease-promoting somatic mutations. Somatic mutations in renal cells can generate genetically distinct cell populations (i.e., subclones) that result in tissue-specific ‘somatic mosaicism’. When these mutations disrupt key epigenetic and transcriptional programs, they can give rise to pathogenic subclones with distinct disease phenotypes and mechanisms. This hypothesis is supported by evidence of increased genomic instability in kidney disease and by the propensity of patients with acute kidney injury or chronic kidney disease to develop renal tumors. However, the role of acquired somatic mosaicism in kidney tissue and its potential pathophysiological implications are incompletely understood. Here, we propose to combine single-cell and strand-specific DNA sequencing (i.e., Strand-seq) with assay for transposase-accessible chromatin (ATAC) and single-nucleus RNA sequencing from kidney cells and tissues to investigate the development and consequences of somatic mosaicism at the single-cell level. We will identify the types and frequency of acquired somatic structural variants such as deletions, insertions, inversions, and other genomic rearrangements and correlate them with changes in genome-wide nucleosome occupancy, chromatin accessibility, and gene expression in kidney cells. We will compare experimental conditions (in vivo ischemia-reperfusion injury in mouse kidneys and in vitro simulated hypoxia of kidney cells) and clinical samples of kidney cells excreted in urine from patients with acute or chronic kidney disease. The putative effects of somatic structural variants on renal cell proliferation, cell death, and gene expression will be validated by experimental modeling of variant-associated molecular perturbations in kidney cells. The study has the potential to uncover novel molecular links between acquired somatic genomic alterations in kidney cells and disease-promoting dysregulation of gene expression control.